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Propranolol-Mediated Attenuation of MMP-9 Excretion in Infants with Hemangiomas
Supplementary Online Content Thaivalappil S, Bauman N, Saieg A, Movius E, Brown KJ, Preciado D. Propranolol-mediated attenuation of MMP-9 excretion in infants with hemangiomas. JAMA Otolaryngol Head Neck Surg. doi:10.1001/jamaoto.2013.4773 eTable. List of All of the Proteins Identified by Proteomics This supplementary material has been provided by the authors to give readers additional information about their work. © 2013 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 10/01/2021 eTable. List of All of the Proteins Identified by Proteomics Protein Name Prop 12 mo/4 Pred 12 mo/4 Δ Prop to Pred mo mo Myeloperoxidase OS=Homo sapiens GN=MPO 26.00 143.00 ‐117.00 Lactotransferrin OS=Homo sapiens GN=LTF 114.00 205.50 ‐91.50 Matrix metalloproteinase‐9 OS=Homo sapiens GN=MMP9 5.00 36.00 ‐31.00 Neutrophil elastase OS=Homo sapiens GN=ELANE 24.00 48.00 ‐24.00 Bleomycin hydrolase OS=Homo sapiens GN=BLMH 3.00 25.00 ‐22.00 CAP7_HUMAN Azurocidin OS=Homo sapiens GN=AZU1 PE=1 SV=3 4.00 26.00 ‐22.00 S10A8_HUMAN Protein S100‐A8 OS=Homo sapiens GN=S100A8 PE=1 14.67 30.50 ‐15.83 SV=1 IL1F9_HUMAN Interleukin‐1 family member 9 OS=Homo sapiens 1.00 15.00 ‐14.00 GN=IL1F9 PE=1 SV=1 MUC5B_HUMAN Mucin‐5B OS=Homo sapiens GN=MUC5B PE=1 SV=3 2.00 14.00 ‐12.00 MUC4_HUMAN Mucin‐4 OS=Homo sapiens GN=MUC4 PE=1 SV=3 1.00 12.00 ‐11.00 HRG_HUMAN Histidine‐rich glycoprotein OS=Homo sapiens GN=HRG 1.00 12.00 ‐11.00 PE=1 SV=1 TKT_HUMAN Transketolase OS=Homo sapiens GN=TKT PE=1 SV=3 17.00 28.00 ‐11.00 CATG_HUMAN Cathepsin G OS=Homo -
Evolution, Expression and Meiotic Behavior of Genes Involved in Chromosome Segregation of Monotremes
G C A T T A C G G C A T genes Article Evolution, Expression and Meiotic Behavior of Genes Involved in Chromosome Segregation of Monotremes Filip Pajpach , Linda Shearwin-Whyatt and Frank Grützner * School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; fi[email protected] (F.P.); [email protected] (L.S.-W.) * Correspondence: [email protected] Abstract: Chromosome segregation at mitosis and meiosis is a highly dynamic and tightly regulated process that involves a large number of components. Due to the fundamental nature of chromosome segregation, many genes involved in this process are evolutionarily highly conserved, but duplica- tions and functional diversification has occurred in various lineages. In order to better understand the evolution of genes involved in chromosome segregation in mammals, we analyzed some of the key components in the basal mammalian lineage of egg-laying mammals. The chromosome passenger complex is a multiprotein complex central to chromosome segregation during both mitosis and meio- sis. It consists of survivin, borealin, inner centromere protein, and Aurora kinase B or C. We confirm the absence of Aurora kinase C in marsupials and show its absence in both platypus and echidna, which supports the current model of the evolution of Aurora kinases. High expression of AURKBC, an ancestor of AURKB and AURKC present in monotremes, suggests that this gene is performing all necessary meiotic functions in monotremes. Other genes of the chromosome passenger complex complex are present and conserved in monotremes, suggesting that their function has been preserved Citation: Pajpach, F.; in mammals. -
Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
(SLC3A2) Sustains Amino Acid and Nucleotide Availability for Cell Cycle
www.nature.com/scientificreports OPEN CD98hc (SLC3A2) sustains amino acid and nucleotide availability for cell cycle progression Received: 16 April 2019 Sara Cano-Crespo1, Josep Chillarón2, Alexandra Junza3,4, Gonzalo Fernández-Miranda1, Accepted: 13 September 2019 Judit García5,6, Christine Polte7, Laura R. de la Ballina 8,9, Zoya Ignatova7, Óscar Yanes 3,4, Published: xx xx xxxx Antonio Zorzano 1,4,10, Camille Stephan-Otto Attolini 1 & Manuel Palacín1,6,10 CD98 heavy chain (CD98hc) forms heteromeric amino acid (AA) transporters by interacting with diferent light chains. Cancer cells overexpress CD98hc-transporters in order to meet their increased nutritional and antioxidant demands, since they provide branched-chain AA (BCAA) and aromatic AA (AAA) availability while protecting cells from oxidative stress. Here we show that BCAA and AAA shortage phenocopies the inhibition of mTORC1 signalling, protein synthesis and cell proliferation caused by CD98hc ablation. Furthermore, our data indicate that CD98hc sustains glucose uptake and glycolysis, and, as a consequence, the pentose phosphate pathway (PPP). Thus, loss of CD98hc triggers a dramatic reduction in the nucleotide pool, which leads to replicative stress in these cells, as evidenced by the enhanced DNA Damage Response (DDR), S-phase delay and diminished rate of mitosis, all recovered by nucleoside supplementation. In addition, proper BCAA and AAA availability sustains the expression of the enzyme ribonucleotide reductase. In this regard, BCAA and AAA shortage results in decreased content of deoxynucleotides that triggers replicative stress, also recovered by nucleoside supplementation. On the basis of our fndings, we conclude that CD98hc plays a central role in AA and glucose cellular nutrition, redox homeostasis and nucleotide availability, all key for cell proliferation. -
Abnormal Spermatogenesis and Reduced Fertility in Transition Nuclear Protein 1-Deficient Mice
Abnormal spermatogenesis and reduced fertility in transition nuclear protein 1-deficient mice Y. Eugene Yu*†,Yun Zhang*, Emmanual Unni*‡, Cynthia R. Shirley*, Jian M. Deng§, Lonnie D. Russell¶, Michael M. Weil*, Richard R. Behringer§, and Marvin L. Meistrich*ʈ Departments of *Experimental Radiation Oncology, and §Molecular Genetics, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030-4095; and ¶Department of Physiology, Southern Illinois University, School of Medicine, Carbondale, IL 62901 Edited by Richard D. Palmiter, University of Washington School of Medicine, Seattle, WA, and approved February 22, 2000 (received for review May 3, 1999) Transition nuclear proteins (TPs), the major proteins found in (15), suggesting some functional relationship between the three chromatin of condensing spermatids, are believed to be important proteins exists. Tnp1, however, is on a separate chromosome and for histone displacement and chromatin condensation during is not clearly related to the other three proteins. mammalian spermatogenesis. We generated mice lacking the ma- In vitro, TP1 decreases the melting temperature of DNA (16) jor TP, TP1, by targeted deletion of the Tnp1 gene in mouse and relaxes the DNA in nucleosomal core particles (17), which embryonic stem cells. Surprisingly, testis weights and sperm pro- led to the proposal that TP1 reduces the interaction of DNA duction were normal in the mutant mice, and only subtle abnor- with the nucleosome core. In contrast, TP2 increases the malities were observed in sperm morphology. Electron microscopy melting temperature of DNA and compacts the DNA in revealed large rod-like structures in the chromatin of mutant step nucleosomal cores, suggesting that it is a DNA-condensing 13 spermatids, in contrast to the fine chromatin fibrils observed in protein (18). -
Supplementary Table 1
Supplementary Table 1. Phosphoryl I-Area II-Area II-Debunker III-Area Gene Symbol Protein Name Phosphorylated Peptide I-R2 I-Debunker score II-R2 III-R2 ation Site Ratio Ratio score Ratio 92154 ABBA-1 Actin-bundling protein with BAIAP2 homologyK.TPTVPDS*PGYMGPTR.A S601 1.76 0.95 0.999958250 1.18 0.98 0.999971836 0.98 0.98 92154 ABBA-1 Actin-bundling protein with BAIAP2 homologyR.AGS*EECVFYTDETASPLAPDLAK.A S612 1.40 0.99 0.999977464 1.03 0.99 0.999986373 1.00 0.99 92154 ABBA-1 Actin-bundling protein with BAIAP2 homologyK.GGGAPWPGGAQTYS*PSSTCR.Y S300 0.49 0.98 0.999985406 0.97 0.99 0.999983906 2.03 0.97 23 ABCF1 ATP-binding cassette sub-family F memberK.QQPPEPEWIGDGESTS*PSDK.V 1 S22 1.09 0.98 0.872361494 0.81 1.00 0.847115585 0.97 0.97 27 ABL2 Isoform IA of Tyrosine-protein kinase ABL2K.VPVLIS*PTLK.H S936 0.76 0.98 0.999991559 1.06 0.99 0.999989547 0.99 0.96 3983 ABLIM1 Actin binding LIM protein 1 R.TLS*PTPSAEGYQDVR.D S433 1.27 0.99 0.999994010 1.16 0.98 0.999989861 1.11 0.99 31 ACACA acetyl-Coenzyme A carboxylase alpha isoformR.FIIGSVSEDNS*EDEISNLVK.L 1 S29 1.23 0.99 0.999992898 0.72 0.99 0.999992499 0.83 0.99 65057 ACD Adrenocortical dysplasia protein homologR.TPS*SPLQSCTPSLSPR.S S424 1.51 0.90 0.999936226 0.82 0.88 0.997623142 0.46 0.93 22985 ACIN1 Apoptotic chromatin condensation inducerK.ASLVALPEQTASEEET*PPPLLTK.E in the nucleus T414 0.90 0.92 0.922696554 0.91 0.92 0.993049132 0.95 0.99 22985 ACIN1 Apoptotic chromatin condensation inducerK.ASLVALPEQTAS*EEETPPPLLTK.E in the nucleus S410 1.02 0.99 0.997470008 0.80 0.99 0.999702808 0.96 -
Lecture9'21 Chromatin II
Genetic Organization -Chromosomal Arrangement: From Form to Function. Chapters 9 & 10 in Genes XI The Eukaryotic chromosome – Organized Structures -banding – Centromeres – Telomeres – Nucleosomes – Euchromatin / Heterochromatin – Higher Orders of Chromosomal Structure 2 Heterochromatin differs from euchromatin in that heterochromatin is effectively inert; remains condensed during interphase; is transcriptionally repressed; replicates late in S phase and may be localized to the centromere or nuclear periphery Facultative heterochromatin is not restricted by pre-designated sequence; genes that are moved within or near heterochromatic regions can become inactivated as a result of their new location. Heterochromatin differs from euchromatin in that heterochromatin is effectively inert; remains condensed during interphase; is transcriptionally repressed; replicates late in S phase and may be localized to the centromere or nuclear periphery Facultative heterochromatin is not restricted by pre-designated sequence; genes that are moved within or near heterochromatic regions can become inactivated as a result of their new location. Chromatin inactivation (or heterochromatin formation) occurs by the addition of proteins to the nucleosomal fiber. May be due to: Chromatin condensation -making it inaccessible to transcriptional apparatus Proteins that accumulate and inhibit accessibility to the regulatory sequences Proteins that directly inhibit transcription Chromatin Is Fundamentally Divided into Euchromatin and Heterochromatin • Individual chromosomes can be seen only during mitosis. • During interphase, the general mass of chromatin is in the form of euchromatin, which is slightly less tightly packed than mitotic chromosomes. TF20210119 Regions of compact heterochromatin are clustered near the nucleolus and nuclear membrane Photo courtesy of Edmund Puvion, Centre National de la Recherche Scientifique Chromatin: Basic Structures • nucleosome – The basic structural subunit of chromatin, consisting of ~200 bp of DNA wrapped around an octamer of histone proteins. -
THE DEVELOPMENT of CHEMICAL METHODS to DISCOVER KINASE SUBSTRATES and MAP CELL SIGNALING with GAMMA-MODIFIED ATP ANALOG-DEPENDENT KINASE-CATALYZED PHOSPHORYLATION By
Wayne State University Wayne State University Dissertations 1-1-2017 The evelopmeD nt Of Chemical Methods To Discover Kinase Substrates And Map Cell Signaling With Gamma-Modified Atp Analog- Dependent Kinase-Catalyzed Phosphorylation Dissanayaka Mudiyanselage Maheeka Madhubashini Embogama Wayne State University, Follow this and additional works at: https://digitalcommons.wayne.edu/oa_dissertations Part of the Analytical Chemistry Commons, and the Biochemistry Commons Recommended Citation Embogama, Dissanayaka Mudiyanselage Maheeka Madhubashini, "The eD velopment Of Chemical Methods To Discover Kinase Substrates And Map Cell Signaling With Gamma-Modified Atp Analog-Dependent Kinase-Catalyzed Phosphorylation" (2017). Wayne State University Dissertations. 1698. https://digitalcommons.wayne.edu/oa_dissertations/1698 This Open Access Dissertation is brought to you for free and open access by DigitalCommons@WayneState. It has been accepted for inclusion in Wayne State University Dissertations by an authorized administrator of DigitalCommons@WayneState. THE DEVELOPMENT OF CHEMICAL METHODS TO DISCOVER KINASE SUBSTRATES AND MAP CELL SIGNALING WITH GAMMA-MODIFIED ATP ANALOG-DEPENDENT KINASE-CATALYZED PHOSPHORYLATION by DISSANAYAKA M. MAHEEKA M. EMBOGAMA DISSERTATION Submitted to the Graduate School of Wayne State University, Detroit, Michigan in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY 2017 MAJOR: CHEMISTRY (Biochemistry) Approved By: Advisor Date DEDICATION To my beloved mother, father, husband, daughter and sister. ii ACKNOWLEGEMENTS Many people have helped me during the past five years of earning my PhD. I would like to take this opportunity to convey my gratitude to them. First and foremost, I would like to thank my research supervisor Dr. Mary Kay Pflum for being the greatest mentor that I have met so far. -